| Methanococcoides burtonii cytochrome b5 domain protein (WP 011499504.1) |
| This entry was created with PDB-REDO version 8.22 using the deposited PDB model version 1.3 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | P 41 2 2 | a: 67.495Å b: 67.495Å c: 48.132Å | α: 90.00° β: 90.00° γ: 90.00° | ||
| Resolution | 2.10 Å | Reflections | 6718 | Test set | 0 (0.0%) |
| R | 0.1620 | R-free | 0.1950 | ||
| According to PDB-REDO | |||||
| Resolution | 2.10 Å | Reflections | 6718 | Test set |
700 (10.4%)
New test set, PDB-REDO compensated for this
|
| Twin | false | Radiation damage | 77 | ||
| PDB-REDO files | |||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
|||
| Links | |||||
| PDBe | RCSB PDB | Proteopedia | |||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.1743 | 0.1680 |
| R-free |
0.2069
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2058 |
| Bond length RMS Z-score | 1.156 | 0.466 |
| Bond angle RMS Z-score | 0.920 | 0.661 |
| Model quality | ||
| Ramachandran plot normality | 0.396 89 | 1.404 97 |
| Rotamer normality | -0.242 86 | 0.044 90 |
| Coarse packing | -0.112 44 | -0.117 43 |
| Fine packing | -1.750 22 | -2.130 11 |
| MolProbity Clashscore | 4.840 55 | 10.480 22 |
| Hydrogen bond satisfaction | 0.864 19 | 0.868 21 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | N/A |
| Side chains built | 0 |
| Waters removed | N/A |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |